Ydc2 protein domain explained

Symbol:	Ydc2-catalyst
Ydc2 protein domain
Pfam:	PF09159
Pfam Clan:	CL0219
Interpro:	IPR015242
Scop:	1kcf
Cdd:	cd00529

In molecular biology, the protein domain, Ydc2 (also known as SpCce1), is a Holliday junction resolvase from the fission yeast Schizosaccharomyces pombe that is involved in the maintenance of mitochondrial DNA.

Function

In molecular biology, the Ydc2 domains are enzymes, or in other words biological catalysts, capable of resolving Holliday junctions into separate DNA duplexes by cleaving DNA after 5'-CT-3, and 5'-TT-3, sequences.

Properties

The junction resolving enzymes are very diverse, but have the following properties in common:

• high structure specificity for binding
• metal dependent, sequence specific cleavage activity^[1]

Essentially, they are highly specific.

Limiting factors

Furthermore, the cleavage efficiency is affected by:

• strand type (continuous or exchange)
• nucleotide sequence at cleavage site^[1]

Structure

This protein domain forms a ribonuclease H fold consisting of two beta sheets and one alpha helix, arranged as a beta-alpha-beta motif. Each beta sheet has five strands, arranged in a 32145 order, with the second strand being antiparallel to the rest.^[2]

Notes and References

1. White MF, Lilley DM . Interaction of the resolving enzyme YDC2 with the four-way DNA junction. . Nucleic Acids Res . 1998 . 26 . 24 . 5609–16 . 9837990 . 10.1093/nar/26.24.5609. 148026 .
2. Ceschini S, Keeley A, McAlister MS, Oram M, Phelan J, Pearl LH, Tsaneva IR, Barrett TE . Crystal structure of the fission yeast mitochondrial Holliday junction resolvase Ydc2 . EMBO J. . 20 . 23 . 6601–11 . December 2001 . 11726496 . 125760 . 10.1093/emboj/20.23.6601 .